Calibration and analysis of the 2007 data

he physics program of the NA61/SHINE (SHINE = SPS Heavy Ion and Neutrino Experiment) experiment at the CERN SPS consists of three subjects. In the first stage of data taking (2007-2009) measurements of hadron production in hadron-nucleus interactions needed for neutrino (T2K) and cosmic-ray (Pierre Auger and KASCADE) experiments will be performed. In the second stage (2009-2010) hadron production in proton-proton and proton-nucleus interactions needed as reference data for a better understanding of nucleus-nucleus reactions will be studied. In the third stage (2009-2013) energy dependence of hadron production properties will be measured in p+p, p+Pb interactions and nucleus-nucleus collisions, with the aim to identify the properties of the onset of deconfinement and find evidence for the critical point of strongly interacting matter. The NA61 experiment was approved at CERN in June 2007. The first pilot run was performed during October 2007. Calibrations of all detector components have been performed successfully and preliminary uncorrected spectra have been obtained. High quality of track reconstruction and particle identification similar to NA49 has been achieved. The data and new detailed simulations confirm that the NA61 detector acceptance and particle identification capabilities cover the phase space required by the T2K experiment. This document reports on the progress made in the calibration and analysis of the 2007 data.

Contingencies for Intercultural Dialogue in Virtual Space: An Empirical Research on the Role of Internet in Fostering Intercultural Competences from the Perspective of Migrant Youth

Against the background of the emerging multicultural migration society, acquisition of intercultural competences is getting vitally important for youngsters to actively and effectively engage with intercultural dialogue in a co-existent life context. Contingencies for such intercultural dialogue and to foster intercultural competences of youngsters are opened in virtual space when youth with different ethnic, social and cultural background go online. However, differences in Internet use and competences acquisition as “digital inequality” also exist among youth with different socio-cultural background. This article reports on a quantitative survey of 300 Turkish migrant youth in Germany as empirical sample about how Internet use generally fosters their intercultural competences, what differences exist among them and which indicators can explain the differences. Preliminary findings show that the contingencies of Internet in fostering intercultural competences are still not much employed and realised by Turkish migrant youth. Four online groups connected with bonding, bridging, both (bonding and bridging) and none socio-cultural networks are found out based on the cluster analysis with SPSS. These different networks, from the perspective of social cultural capital, can explain the differences concerning development of intercultural competences among them. It is indicated in this research that many Turkish migrant youth still lack recognition and capabilities to construct their intercultural social networks or relations through using Internet and further to employ the relations as intercultural social capital or social support in their life context. This therefore poses a critical implication for youth work to help migrant youth construct and reconstruct their socio-cultural networks through using Internet so as to extend social support for competences acquisition.

Clinical and pathological analysis of epidural inflammation in intervertebral disk extrusion in dogs

BACKGROUND Little is known about the pathologic changes in the epidural space after intervertebral disk (IVD) extrusion in the dog. OBJECTIVES To analyze the pathology of the epidural inflammatory response, and to search for correlations between this process and clinical findings. METHODS Clinical data from 105 chondrodystrophic (CD) and nonchondrodystrophic (NCD) dogs with IVD extrusion were recorded. Epidural material from these dogs was examined histopathologically and immunohistochemically. Using statistical analysis, we searched for correlations between severity of epidural inflammation and various clinical and pathologic variables. RESULTS Most dogs exhibited an epidural inflammatory response, ranging from acute invasion of neutrophils to formation of chronic granulation tissue. The mononuclear inflammatory infiltrates consisted mostly of monocytes and macrophages and only few T and B cells. Surprisingly, chronic inflammatory patterns also were found in animals with an acute clinical history. Severity of the epidural inflammation correlated with degree of the epidural hemorrhage and nucleus pulposus calcification (P = .003 and .040), but not with age, chondrodystrophic phenotype, neurologic grade, back pain, pretreatment, or duration. The degree of inflammation was statistically (P = .021) inversely correlated with the ability to regain ambulation. CONCLUSION AND CLINICAL IMPORTANCE Epidural inflammation occurs in the majority of dogs with IVD extrusion and may develop long before the onset of clinical signs. Presence of calcified IVD material and hemorrhage in the epidural space may be the triggers of this lesion rather than an adaptive immune response to the nucleus pulposus as suggested in previous studies. Because epidural inflammation may affect outcome, further research is warranted.

ANOVA kernels and RKHS of zero mean functions for model-based sensitivity analysis

Given a reproducing kernel Hilbert space (H,〈.,.〉)(H,〈.,.〉) of real-valued functions and a suitable measure μμ over the source space D⊂RD⊂R, we decompose HH as the sum of a subspace of centered functions for μμ and its orthogonal in HH. This decomposition leads to a special case of ANOVA kernels, for which the functional ANOVA representation of the best predictor can be elegantly derived, either in an interpolation or regularization framework. The proposed kernels appear to be particularly convenient for analyzing the effect of each (group of) variable(s) and computing sensitivity indices without recursivity.

Space, diffusion and mobility

Given its origins in traditional dialectology, and given advances in our understanding of the social embedding of language variation, it is paradoxical that space should be one of the categories that has received least attention of all in variationist sociolinguistics. Until recently, space has largely been treated as an empty stage on which sociolinguistic processes are enacted. It has been unexamined, untheorized, and its role in shaping and being shaped by variation and change untested. One function of this chapter, therefore, is to assert that space makes a difference, and to begin, in a very hesitant way, to map out what a geographically informed variation analysis might need to address. It also examines variationist interactions with the related concept of mobility. It might be reasonable to think that human geographers would provide some clues on how to proceed. As we will see, they have engaged in a great deal of soul searching about the goals of their discipline, its very existence as a separate field of enquiry, and the directions it should take. Indeed there are remarkable parallels between the recent history of human geographic thought, and interest in language variation across space. Although space has been undertheorized in variation studies, a number of researchers, from the traditional dialectologists through to those interested in the dialectology of mobility and contact, have, of course, been actively engaged in research on geographical variation and language use. Their work will be contextualized here to highlight both the parallels with theory-building in human geography, but also some of the criticisms of earlier approaches which have fed through to human geography, but remain largely unquestioned in variationist practice. The chapter therefore presents a brief theoretical background to space and mobility, before exemplifying these concepts in variationist research through an examination of, for example, the spatial diffusion of linguistic innovations, the spatial configuration of linguistic boundaries and initial steps to examine the consequences of mobility for variationist research.

Test Facility to Study Surface-Interaction Processes for Particle Detection in Space

The Imager for Low Energetic Neutral Atoms test facility at the University of Bern was developed to investigate, characterize, and quantify physical processes on surfaces that are used to ionize neutral atoms before their analysis in neutral particle-sensing instruments designed for space research. The facility has contributed valuable knowledge of the interaction of ions with surfaces (e.g., fraction of ions scattered from surfaces and angular scattering distribution) and employs a novel measurement principle for the determination of secondary electron emission yields as a function of energy, angle of incidence, particle species, and sample surface for low particle energies. Only because of this test facility it was possible to successfully apply surface-science processes for the new detection technique for low-energetic neutral particles with energies below about 1 keV used in space applications. All successfully flown spectrometers for the detection of low-energetic neutrals based on the particle–surface interaction process use surfaces evaluated, tested, and calibrated in this facility. Many instruments placed on different spacecraft (e.g., Imager for Magnetopause-to-Aurora Global Exploration, Chandrayaan-1, Interstellar Boundary Explorer, etc.) have successfully used this technique.

Microscopic analysis of chromatin localization and dynamics in C. elegans

During development, the genome undergoes drastic reorganization within the nuclear space. To determine tridimensional genome folding, genome-wide techniques (damID/Hi-C) can be applied using cell populations, but these have to be calibrated using microscopy and single-cell analysis of gene positioning. Moreover, the dynamic behavior of chromatin has to be assessed on living samples. Combining fast stereotypic development with easy genetics and microscopy, the nematode C. elegans has become a model of choice in recent years to study changes in nuclear organization during cell fate acquisition. Here we present two complementary techniques to evaluate nuclear positioning of genes either by fluorescence in situ hybridization in fixed samples or in living worm embryos using the GFP-lacI/lacO chromatin-tagging system.

Evaluating the disparity of female breast cancer mortality among racial groups - a spatiotemporal analysis

Background The literature suggests that the distribution of female breast cancer mortality demonstrates spatial concentration. There remains a lack of studies on how the mortality burden may impact racial groups across space and over time. The present study evaluated the geographic variations in breast cancer mortality in Texas females according to three predominant racial groups (non-Hispanic White, Black, and Hispanic females) over a twelve-year period. It sought to clarify whether the spatiotemporal trend might place an uneven burden on particular racial groups, and whether the excess trend has persisted into the current decade. Methods The Spatial Scan Statistic was employed to examine the geographic excess of breast cancer mortality by race in Texas counties between 1990 and 2001. The statistic was conducted with a scan window of a maximum of 90% of the study period and a spatial cluster size of 50% of the population at risk. The next scan was conducted with a purely spatial option to verify whether the excess mortality persisted further. Spatial queries were performed to locate the regions of excess mortality affecting multiple racial groups. Results The first scan identified 4 regions with breast cancer mortality excess in both non-Hispanic White and Hispanic female populations. The most likely excess mortality with a relative risk of 1.12 (p = 0.001) occurred between 1990 and 1996 for non-Hispanic Whites, including 42 Texas counties along Gulf Coast and Central Texas. For Hispanics, West Texas with a relative risk of 1.18 was the most probable region of excess mortality (p = 0.001). Results of the second scan were identical to the first. This suggested that the excess mortality might not persist to the present decade. Spatial queries found that 3 counties in Southeast and 9 counties in Central Texas had excess mortality involving multiple racial groups. Conclusion Spatiotemporal variations in breast cancer mortality affected racial groups at varying levels. There was neither evidence of hot-spot clusters nor persistent spatiotemporal trends of excess mortality into the present decade. Non-Hispanic Whites in the Gulf Coast and Hispanics in West Texas carried the highest burden of mortality, as evidenced by spatial concentration and temporal persistence.

Bifurcation and singularity analysis of a molecular network for the induction of long-term memory.

Withdrawal reflexes of the mollusk Aplysia exhibit sensitization, a simple form of long-term memory (LTM). Sensitization is due, in part, to long-term facilitation (LTF) of sensorimotor neuron synapses. LTF is induced by the modulatory actions of serotonin (5-HT). Pettigrew et al. developed a computational model of the nonlinear intracellular signaling and gene network that underlies the induction of 5-HT-induced LTF. The model simulated empirical observations that repeated applications of 5-HT induce persistent activation of protein kinase A (PKA) and that this persistent activation requires a suprathreshold exposure of 5-HT. This study extends the analysis of the Pettigrew model by applying bifurcation analysis, singularity theory, and numerical simulation. Using singularity theory, classification diagrams of parameter space were constructed, identifying regions with qualitatively different steady-state behaviors. The graphical representation of these regions illustrates the robustness of these regions to changes in model parameters. Because persistent protein kinase A (PKA) activity correlates with Aplysia LTM, the analysis focuses on a positive feedback loop in the model that tends to maintain PKA activity. In this loop, PKA phosphorylates a transcription factor (TF-1), thereby increasing the expression of an ubiquitin hydrolase (Ap-Uch). Ap-Uch then acts to increase PKA activity, closing the loop. This positive feedback loop manifests multiple, coexisting steady states, or multiplicity, which provides a mechanism for a bistable switch in PKA activity. After the removal of 5-HT, the PKA activity either returns to its basal level (reversible switch) or remains at a high level (irreversible switch). Such an irreversible switch might be a mechanism that contributes to the persistence of LTM. The classification diagrams also identify parameters and processes that might be manipulated, perhaps pharmacologically, to enhance the induction of memory. Rational drug design, to affect complex processes such as memory formation, can benefit from this type of analysis.

An Extended Hierarchical Task Analysis for Error Prediction in Medical Devices

This paper introduces an extended hierarchical task analysis (HTA) methodology devised to evaluate and compare user interfaces on volumetric infusion pumps. The pumps were studied along the dimensions of overall usability and propensity for generating human error. With HTA as our framework, we analyzed six pumps on a variety of common tasks using Norman’s Action theory. The introduced method of evaluation divides the problem space between the external world of the device interface and the user’s internal cognitive world, allowing for predictions of potential user errors at the human-device level. In this paper, one detailed analysis is provided as an example, comparing two different pumps on two separate tasks. The results demonstrate the inherent variation, often the cause of usage errors, found with infusion pumps being used in hospitals today. The reported methodology is a useful tool for evaluating human performance and predicting potential user errors with infusion pumps and other simple medical devices.

Extended kalman filter for estimation of parameters in nonlinear state-space models of biochemical networks.

It is system dynamics that determines the function of cells, tissues and organisms. To develop mathematical models and estimate their parameters are an essential issue for studying dynamic behaviors of biological systems which include metabolic networks, genetic regulatory networks and signal transduction pathways, under perturbation of external stimuli. In general, biological dynamic systems are partially observed. Therefore, a natural way to model dynamic biological systems is to employ nonlinear state-space equations. Although statistical methods for parameter estimation of linear models in biological dynamic systems have been developed intensively in the recent years, the estimation of both states and parameters of nonlinear dynamic systems remains a challenging task. In this report, we apply extended Kalman Filter (EKF) to the estimation of both states and parameters of nonlinear state-space models. To evaluate the performance of the EKF for parameter estimation, we apply the EKF to a simulation dataset and two real datasets: JAK-STAT signal transduction pathway and Ras/Raf/MEK/ERK signaling transduction pathways datasets. The preliminary results show that EKF can accurately estimate the parameters and predict states in nonlinear state-space equations for modeling dynamic biochemical networks.

Hebbian analysis of the transformation of medial entorhinal grid-cell inputs to hippocampal place fields.

The discovery of grid cells in the medial entorhinal cortex (MEC) permits the characterization of hippocampal computation in much greater detail than previously possible. The present study addresses how an integrate-and-fire unit driven by grid-cell spike trains may transform the multipeaked, spatial firing pattern of grid cells into the single-peaked activity that is typical of hippocampal place cells. Previous studies have shown that in the absence of network interactions, this transformation can succeed only if the place cell receives inputs from grids with overlapping vertices at the location of the place cell's firing field. In our simulations, the selection of these inputs was accomplished by fast Hebbian plasticity alone. The resulting nonlinear process was acutely sensitive to small input variations. Simulations differing only in the exact spike timing of grid cells produced different field locations for the same place cells. Place fields became concentrated in areas that correlated with the initial trajectory of the animal; the introduction of feedback inhibitory cells reduced this bias. These results suggest distinct roles for plasticity of the perforant path synapses and for competition via feedback inhibition in the formation of place fields in a novel environment. Furthermore, they imply that variability in MEC spiking patterns or in the rat's trajectory is sufficient for generating a distinct population code in a novel environment and suggest that recalling this code in a familiar environment involves additional inputs and/or a different mode of operation of the network.